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- PDB-5n0i: Crystal structure of NDM-1 in complex with beta-mercaptoethanol -... -

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Basic information

Entry
Database: PDB / ID: 5n0i
TitleCrystal structure of NDM-1 in complex with beta-mercaptoethanol - new refinement
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE / NDM-1 / metallo-beta-lactamase
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsRaczynska, J.E. / Shabalin, I.G. / Jaskolski, M. / Minor, W. / Wlodawer, A. / King, D.T. / Strynadka, N.C.J.
CitationJournal: Drug Resist. Updat. / Year: 2018
Title: A close look onto structural models and primary ligands of metallo-beta-lactamases.
Authors: Raczynska, J.E. / Shabalin, I.G. / Minor, W. / Wlodawer, A. / Jaskolski, M.
History
DepositionFeb 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Remark 0THIS ENTRY 5N0I REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R4EXYSF) ...THIS ENTRY 5N0I REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R4EXYSF) DETERMINED BY AUTHORS OF THE PDB ENTRY 4EXY: D.T.KING, N.C.J.STRYNADKA ORIGINAL DATA REFERENCE 1 PDB ID: 4EXY AUTH D.T.KING,L.J.WORRALL,R.GRUNINGER,N.C.STRYNADKA TITL NEW DELHI METALLO-BETA-LACTAMASE: STRUCTURAL INSIGHTS INTO TITL 2 BETA-LACTAM RECOGNITION AND INHIBITION REF J.AM.CHEM.SOC. V. 134 11362 2012 REFN ISSN 0002-7863 PMID 22713171 DOI 10.1021/JA303579D

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallo-beta-lactamase type 2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,67213
Polymers51,7482
Non-polymers92411
Water10,233568
1
A: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2676
Polymers25,8741
Non-polymers3935
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4057
Polymers25,8741
Non-polymers5316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.220, 107.220, 92.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Metallo-beta-lactamase type 2 / B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta- ...B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta-lactamase type II / New Delhi metallo-beta-lactamase-1 / NDM-1


Mass: 25874.160 Da / Num. of mol.: 2 / Fragment: UNP Residues 29-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: C7C422, beta-lactamase

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Non-polymers , 6 types, 579 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 568 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% w/v PEG8K, 8% w/v ethylene glycol, 0.1M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 22, 2011
RadiationMonochromator: TEROIDAL FOCUSING MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.47→35.74 Å / Num. obs: 91755 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rsym value: 0.06 / Net I/σ(I): 10.6
Reflection shellResolution: 1.47→1.55 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3 / Rsym value: 0.372 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→35.74 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.827 / SU ML: 0.03 / Cross valid method: FREE R-VALUE / ESU R: 0.048 / ESU R Free: 0.048 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14735 4592 5 %copied from 4exy
Rwork0.10956 ---
obs0.11145 87106 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.599 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0 Å20 Å2
2---0.2 Å20 Å2
3---0.4 Å2
Refinement stepCycle: 1 / Resolution: 1.47→35.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3497 0 36 568 4101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193731
X-RAY DIFFRACTIONr_bond_other_d0.0020.023502
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.9435094
X-RAY DIFFRACTIONr_angle_other_deg1.04638058
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8495504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30124.813160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.18715567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6341516
X-RAY DIFFRACTIONr_chiral_restr0.1130.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214338
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02842
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1131.4971920
X-RAY DIFFRACTIONr_mcbond_other3.0581.4961919
X-RAY DIFFRACTIONr_mcangle_it3.9182.2552405
X-RAY DIFFRACTIONr_mcangle_other3.9362.2562406
X-RAY DIFFRACTIONr_scbond_it4.2971.8491811
X-RAY DIFFRACTIONr_scbond_other4.2961.8491811
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7892.6052673
X-RAY DIFFRACTIONr_long_range_B_refined5.93714.8934603
X-RAY DIFFRACTIONr_long_range_B_other5.93760.6334604
X-RAY DIFFRACTIONr_rigid_bond_restr2.1737224
X-RAY DIFFRACTIONr_sphericity_free34.8015166
X-RAY DIFFRACTIONr_sphericity_bonded12.06157525
LS refinement shellResolution: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 327 -
Rwork0.19 6170 -
obs--96.74 %

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